Gadolinium in PDB 8uqz: Round 18 Arylesterase Variant of Phosphotriesterase Bound to Gadolinium(III) Measured at 9.5 Kev

The structure of Round 18 Arylesterase Variant of Phosphotriesterase Bound to Gadolinium(III) Measured at 9.5 Kev, PDB code: 8uqz was solved by C.W.Breeze, R.L.Frkic, E.C.Campbell, C.J.Jackson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.86 / 1.61
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.714, 86.138, 89.247, 90, 90, 90
R / Rfree (%)	17 / 19.5

The structure of Round 18 Arylesterase Variant of Phosphotriesterase Bound to Gadolinium(III) Measured at 9.5 Kev also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Gadolinium atom in the Round 18 Arylesterase Variant of Phosphotriesterase Bound to Gadolinium(III) Measured at 9.5 Kev (pdb code 8uqz). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total only one binding site of Gadolinium was determined in the Round 18 Arylesterase Variant of Phosphotriesterase Bound to Gadolinium(III) Measured at 9.5 Kev, PDB code: 8uqz:

Gadolinium binding site 1 out of 1 in the Round 18 Arylesterase Variant of Phosphotriesterase Bound to Gadolinium(III) Measured at 9.5 Kev


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Round 18 Arylesterase Variant of Phosphotriesterase Bound to Gadolinium(III) Measured at 9.5 Kev within 5.0Å range: probe atom residue distance (Å) B Occ A:Gd403 b:26.8 occ:0.24 OD1 A:ASP301 2.3 26.2 1.0 O A:HOH607 2.4 31.6 1.0 NE2 A:HIS57 2.4 21.7 1.0 HM2 A:MPD402 2.7 50.9 1.0 H51 A:MPD402 2.8 67.6 1.0 NE2 A:HIS55 2.8 27.9 1.0 OD2 A:ASP301 2.8 31.4 1.0 CL A:CL404 2.8 31.8 0.8 CG A:ASP301 2.9 26.3 1.0 H52 A:MPD402 2.9 67.6 1.0 HE1 A:HIS57 3.0 28.4 1.0 HM1 A:MPD402 3.0 50.9 1.0 CE1 A:HIS57 3.0 23.6 1.0 C5 A:MPD402 3.3 56.3 1.0 CM A:MPD402 3.3 42.4 1.0 HD2 A:HIS55 3.5 25.3 1.0 CD2 A:HIS55 3.6 21.1 1.0 CD2 A:HIS57 3.6 21.2 1.0 H53 A:MPD402 3.8 67.6 1.0 HZ1 A:LYS169 3.9 40.0 0.4 CE1 A:HIS55 3.9 25.0 1.0 HZ2 A:LYS169 3.9 40.0 0.4 HD2 A:HIS57 4.0 25.5 1.0 HM3 A:MPD402 4.0 50.9 1.0 HG21 A:VAL101 4.2 25.1 1.0 HE1 A:HIS55 4.2 30.1 1.0 O A:HOH591 4.2 36.4 1.0 HG23 A:VAL101 4.2 25.1 1.0 ND1 A:HIS57 4.3 20.4 1.0 NZ A:LYS169 4.3 33.3 0.4 NE2 A:HIS230 4.4 34.6 1.0 CB A:ASP301 4.4 22.0 1.0 HH11 A:ARG254 4.4 52.5 1.0 C2 A:MPD402 4.5 45.4 1.0 H31 A:MPD402 4.5 65.8 1.0 CG2 A:VAL101 4.6 20.9 1.0 C4 A:MPD402 4.6 60.0 1.0 HE2 A:LYS169 4.6 39.0 0.6 CG A:HIS57 4.6 18.7 1.0 HA A:ASP301 4.6 25.1 1.0 HZ3 A:LYS169 4.6 40.0 0.4 HG22 A:VAL101 4.7 25.1 1.0 HD21 A:LEU106 4.7 30.3 1.0 HE1 A:HIS230 4.7 44.5 1.0 HB2 A:ASP301 4.8 26.5 1.0 C3 A:MPD402 4.8 54.8 1.0 O2 A:MPD402 4.8 40.9 1.0 CG A:HIS55 4.8 20.1 1.0 HE1 A:HIS201 4.9 36.6 1.0 HB3 A:ASP301 4.9 26.5 1.0 HH12 A:ARG254 4.9 52.5 1.0 ND1 A:HIS55 5.0 41.9 1.0 CE1 A:HIS230 5.0 37.1 1.0 HD1 A:HIS57 5.0 24.5 1.0 HZ1 A:LYS169 5.0 35.3 0.6 HE1 A:TRP131 5.0 31.4 1.0

C.W.Breeze, Y.Nakano, E.C.Campbell, R.L.Frkic, D.W.Lupton, C.J.Jackson. Mononuclear Binding and Catalytic Activity of Europium(III) and Gadolinium(III) at the Active Site of the Model Metalloenzyme Phosphotriesterase. Acta Crystallogr D Struct 2024BIOL.
ISSN: ISSN 2059-7983
PubMed: 38512071
DOI: 10.1107/S2059798324002316